5DCQ
Crystal structure of bacterial adhesin, FNE from Streptococcus equi spp. equi.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277.15 | magnesium formate, PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 113.688 | α = 90 |
b = 113.688 | β = 90 |
c = 152.623 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 153 | PIXEL | DECTRIS PILATUS 6M | 2012-02-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.972 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 1.83 | 50 | 97.78 | 0.06 | 14.2 | 2.3 | 91861 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.83 | 1.94 | 97.7 | 0.642 | 1.9 | 2.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2XI9, 3LTJ | 1.83 | 50 | 96630 | 4769 | 97.78 | 0.1688 | 0.1671 | 0.2025 | RANDOM | 19.445 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.21 | 0.1 | 0.21 | -0.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.56 |
r_dihedral_angle_3_deg | 15.02 |
r_dihedral_angle_4_deg | 14.041 |
r_dihedral_angle_1_deg | 5.693 |
r_mcangle_it | 2.946 |
r_mcbond_other | 2.378 |
r_mcbond_it | 2.377 |
r_angle_refined_deg | 1.501 |
r_angle_other_deg | 1.338 |
r_chiral_restr | 0.091 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8507 |
Nucleic Acid Atoms | |
Solvent Atoms | 1102 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |